Magnesium in PDB 5x7u: Trehalose Synthase From Thermobaculum Terrenum

The structure of Trehalose Synthase From Thermobaculum Terrenum, PDB code: 5x7u was solved by J.Su, F.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.79 / 2.50
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	159.176, 159.176, 152.815, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.9

The binding sites of Magnesium atom in the Trehalose Synthase From Thermobaculum Terrenum (pdb code 5x7u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Trehalose Synthase From Thermobaculum Terrenum, PDB code: 5x7u:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Trehalose Synthase From Thermobaculum Terrenum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trehalose Synthase From Thermobaculum Terrenum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:33.0 occ:1.00 OD1 A:ASP23 2.2 35.7 1.0 O A:SER29 2.3 39.9 1.0 OD2 A:ASP31 2.3 32.3 1.0 OD1 A:ASN25 2.3 44.1 1.0 OD1 A:ASP27 2.4 41.0 1.0 CG A:ASP27 3.2 36.9 1.0 OD2 A:ASP27 3.3 42.4 1.0 CG A:ASP23 3.3 36.1 1.0 CG A:ASP31 3.4 34.5 1.0 CG A:ASN25 3.4 39.1 1.0 C A:SER29 3.4 34.9 1.0 CB A:ASP31 3.8 30.3 1.0 ND2 A:ASN25 3.9 37.0 1.0 OD2 A:ASP23 4.1 30.3 1.0 O A:ASP76 4.2 42.7 1.0 N A:SER29 4.2 33.5 1.0 C A:GLY30 4.2 35.8 1.0 CA A:ASP23 4.2 31.9 1.0 CA A:SER29 4.2 30.5 1.0 CB A:ASP23 4.2 33.9 1.0 N A:ASN25 4.3 33.9 1.0 O A:GLY30 4.3 36.9 1.0 N A:SER24 4.3 37.4 1.0 N A:ASP31 4.4 32.5 1.0 CB A:SER29 4.4 40.2 1.0 N A:GLY30 4.4 37.9 1.0 N A:ASP27 4.5 30.1 1.0 OD1 A:ASP31 4.5 33.8 1.0 CA A:GLY30 4.5 37.9 1.0 CB A:ASP27 4.6 30.7 1.0 C A:ASP23 4.6 35.4 1.0 CB A:ASN25 4.6 30.4 1.0 N A:ASN26 4.7 35.5 1.0 OG A:SER29 4.7 48.4 1.0 CA A:ASP31 4.7 35.4 1.0 CA A:ASN25 4.9 33.7 1.0 C A:ASN25 5.0 38.3 1.0 CA A:ASP27 5.0 31.6 1.0

Magnesium binding site 2 out of 4 in the Trehalose Synthase From Thermobaculum Terrenum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trehalose Synthase From Thermobaculum Terrenum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:34.0 occ:1.00 NH2 A:ARG471 2.9 56.4 1.0 NE A:ARG283 3.5 36.2 1.0 O A:HOH808 3.6 47.6 1.0 OG1 A:THR287 3.6 33.8 1.0 NH2 A:ARG291 3.7 50.4 1.0 NH1 A:ARG471 3.8 57.1 1.0 CZ A:ARG471 3.8 53.5 1.0 OE1 A:GLN467 4.1 58.7 1.0 NH1 A:ARG291 4.2 53.7 1.0 CD A:ARG283 4.2 34.2 1.0 CD2 A:HIS284 4.2 50.5 1.0 NH2 A:ARG283 4.4 39.0 1.0 CG A:GLN467 4.4 50.1 1.0 CZ A:ARG283 4.4 36.0 1.0 CZ A:ARG291 4.4 50.7 1.0 CG A:ARG283 4.5 31.9 1.0 CB A:THR287 4.5 36.5 1.0 CD A:GLN467 4.8 66.2 1.0 CG2 A:THR287 4.9 30.8 1.0

Magnesium binding site 3 out of 4 in the Trehalose Synthase From Thermobaculum Terrenum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trehalose Synthase From Thermobaculum Terrenum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:48.7 occ:1.00 NH1 A:ARG355 2.6 39.0 1.0 O A:HOH873 2.9 44.9 1.0 CD2 A:HIS534 3.1 30.6 1.0 NE2 A:HIS534 3.7 30.5 1.0 OG A:SER352 3.7 33.0 1.0 CZ A:ARG355 3.7 51.1 1.0 NH2 A:ARG355 4.1 46.9 1.0 O A:HOH921 4.2 56.4 1.0 NE A:ARG354 4.2 57.5 1.0 CG A:HIS534 4.4 29.8 1.0 NH2 A:ARG354 4.4 55.1 1.0 CB A:ARG354 4.5 32.1 1.0 CZ A:ARG354 4.6 57.1 1.0 NE A:ARG355 4.7 35.4 1.0 CB A:SER352 4.7 30.4 1.0 CB A:PRO533 4.7 30.2 1.0 CB A:ARG493 4.9 29.2 1.0 CG A:ARG355 4.9 28.6 1.0 CE1 A:HIS534 4.9 27.3 1.0

Magnesium binding site 4 out of 4 in the Trehalose Synthase From Thermobaculum Terrenum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Trehalose Synthase From Thermobaculum Terrenum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:33.9 occ:1.00 OD2 A:ASP172 2.3 46.5 1.0 OE1 A:GLU209 2.4 48.6 1.0 O A:TYR206 2.4 49.5 1.0 O A:LEU207 2.4 43.5 1.0 OD1 A:ASN104 2.7 47.9 1.0 CG A:ASP172 3.3 44.7 1.0 C A:LEU207 3.3 45.8 1.0 CD A:GLU209 3.4 51.8 1.0 C A:TYR206 3.5 41.9 1.0 CG A:ASN104 3.6 39.6 1.0 CB A:ASP172 3.6 39.9 1.0 OE2 A:GLU209 3.7 51.0 1.0 CA A:LEU207 3.7 44.7 1.0 ND2 A:ASN104 3.9 34.4 1.0 O A:ASN104 4.0 44.3 1.0 O A:LEU173 4.0 51.0 1.0 N A:LEU207 4.1 39.1 1.0 O A:HOH759 4.3 44.3 1.0 OD1 A:ASP172 4.4 44.1 1.0 N A:TYR208 4.5 46.0 1.0 NE1 A:TRP163 4.5 43.4 1.0 CD1 A:TRP163 4.7 43.2 1.0 CA A:TYR206 4.7 41.9 1.0 CB A:TYR206 4.7 40.4 1.0 CA A:ASP172 4.8 41.0 1.0 CG A:GLU209 4.8 48.8 1.0 CB A:ASN104 4.8 34.7 1.0 C A:ASN104 4.9 42.0 1.0

J.Wang, X.Ren, R.Wang, J.Su, F.Wang. Structural Characteristics and Function of A New Kind of Thermostable Trehalose Synthase From Thermobaculum Terrenum. J. Agric. Food Chem. V. 65 7726 2017.
ISSN: ESSN 1520-5118
PubMed: 28809106
DOI: 10.1021/ACS.JAFC.7B02732